*sigh* Every time you beat a boss, and some portion of the story, a little thing will come up that looks exactly like what happens when you level up (Where it shows you which stat went up, and if you got a new ability), only instead of it saying 'Level up!' it says 'Get bonus!'
So when you beat boss's, you usually get a 'Get Bonus', and you get a new ability, or item, or keyblade. Every time you get a 'Get Bonus!' your Bonus Level goes up
The Bonus Level just shows how much you've achieved. If you're at the Final Battle and your Bonus Level is only at, say 45, then you skipped some things and you're missing some abilties
And yes, it maxes at 50